GeneBe

rs61507713

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_174932.3(BPIFC):​c.531-27_531-16delTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000788 in 634,714 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000079 ( 0 hom. )

Consequence

BPIFC
NM_174932.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.416
Variant links:
Genes affected
BPIFC (HGNC:16503): (BPI fold containing family C) Predicted to enable lipid binding activity. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BPIFCNM_174932.3 linkc.531-27_531-16delTTTTTTTTTTTT intron_variant Intron 6 of 16 ENST00000300399.9 NP_777592.1 Q8NFQ6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BPIFCENST00000300399.9 linkc.531-27_531-16delTTTTTTTTTTTT intron_variant Intron 6 of 16 1 NM_174932.3 ENSP00000300399.3 Q8NFQ6-1
BPIFCENST00000397452.5 linkc.531-27_531-16delTTTTTTTTTTTT intron_variant Intron 5 of 15 5 ENSP00000380594.1 Q8NFQ6-1
BPIFCENST00000534972.4 linkn.*236-27_*236-16delTTTTTTTTTTTT intron_variant Intron 5 of 14 5 ENSP00000439123.3 A0A8C8NLL8

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000788
AC:
5
AN:
634714
Hom.:
0
AF XY:
0.00000935
AC XY:
3
AN XY:
320838
show subpopulations
Gnomad4 AFR exome
AF:
0.0000610
Gnomad4 AMR exome
AF:
0.000137
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000420
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000210
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-32841700; API